Previously ultrastructural studies have shown that B. pertussis has a crystalline surface lattice consisting of a 40 kDa porin protein. We have developed large scale methods for the purification of this protein in order to study the structural and functional characteristics of this protein. Porin protein was purified by sequential extractions of cell envelopes with Triton X-100 and Zwittergent 3-14 followed by DEAE ion-exchange chromatography. NH2-terminal amino acid analysis of the purified porin was performed and an oligonucleotide was constructed from this sequence. This oligo was used to probe a lgt11 library of B. pertussis DNA and a clone was identified that consists of a truncated porin gene containing the N-terminal portion of the protein. This gene sequence was ued to design an additional oligonucleotide that was used to identify a second clone which overlapped with the first clone and contained a termination condon. The structural gene deduced from this sequence would encode a 365 amino-acid polypeptide with a predicted mass of 39103 daltons. The predicted B. pertussis porin protein sequence contains regions that are homologous to regions found in porins expressed by Neisseria species and Escherichia coli, including the presence of phenylalaine as the carboxy-terminal amino acid. DNA hybridization studies indicated that both virulent and avirulent strains of B. pertussis contain only one copy of this gene and that Bordetella bronchiseptica and Bordetella parapertussis contain a similar gene. Identification of the porin gene will allow further molecular studies on the structure and function of this outer membrane protein.